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Detailed information for vg0611474489:

Variant ID: vg0611474489 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11474489
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


AGCCCACGTGGGCCCCCACATGTCATTCTCATTCCCCTCTTCTCTCTCCCCTCTACCCCGGGCAGTCTTCTTCCTCCTCTCTCCCTACTCCTCTCTGAGA[C/T]
GGTGGAAGAGAGGGTTGACAACGCTCCCTACGCCTCTCTCCTTCCCCTTTTCGGCATATGGGTAGAAGAGGACGAAGCCATAGCCCTTAGATCTACCAGA

Reverse complement sequence

TCTGGTAGATCTAAGGGCTATGGCTTCGTCCTCTTCTACCCATATGCCGAAAAGGGGAAGGAGAGAGGCGTAGGGAGCGTTGTCAACCCTCTCTTCCACC[G/A]
TCTCAGAGAGGAGTAGGGAGAGAGGAGGAAGAAGACTGCCCGGGGTAGAGGGGAGAGAGAAGAGGGGAATGAGAATGACATGTGGGGGCCCACGTGGGCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 1.10% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 83.60% 16.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0611474489 C -> T LOC_Os06g20010.1 missense_variant ; p.Arg85His; MODERATE nonsynonymous_codon ; R85H Average:71.007; most accessible tissue: Zhenshan97 young leaf, score: 88.127 unknown unknown TOLERATED 0.21